Add BitRound filter and its plugin ID 32032

.github/workflows/main-fetchcontent-mac.yml

@@ -83,6 +83,7 @@ jobs:
             -DENABLE_ZSTD=OFF \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             ..
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
@@ -166,6 +167,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
@@ -241,6 +243,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}

.github/workflows/main-fetchcontent-ubuntu.yml

@@ -78,6 +78,7 @@ jobs:
             -DENABLE_ZSTD=OFF \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             ..
           # NOTE: Currently a serial build has to be forced, as Blosc and Blosc2
@@ -158,6 +159,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           # NOTE: Currently, a serial build has to be forced as Blosc and Blosc2
@@ -235,6 +237,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           # NOTE: Currently, a serial build has to be forced as Blosc and Blosc2

.github/workflows/main-fetchcontent-win.yml

@@ -87,6 +87,7 @@ jobs:
             -DENABLE_ZSTD=OFF \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             ..
           cmake --build . --parallel 4 --config ${{ inputs.build_mode }}
@@ -175,6 +176,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 4 --config ${{ inputs.build_mode }}
@@ -261,6 +263,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=ON \
             -DENABLE_GRANULAR_BITROUND=ON \
+            -DENABLE_BITROUND=ON \
             -DENABLE_BSHUF=ON \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 4 --config ${{ inputs.build_mode }}

.github/workflows/main-package-managers-mac.yml

@@ -123,6 +123,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=OFF \
             -DENABLE_GRANULAR_BITROUND=OFF \
+            -DENABLE_BITROUND=OFF \
             -DENABLE_BSHUF=OFF \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 3 --config ${{ inputs.build_mode }}

.github/workflows/main-package-managers-ubuntu.yml

@@ -97,6 +97,7 @@ jobs:
             -DENABLE_ZFP=OFF \
             -DENABLE_BITGROOM=OFF \
             -DENABLE_GRANULAR_BITROUND=OFF \
+            -DENABLE_BITROUND=OFF \
             -DENABLE_BLOSC=OFF \
             -DENABLE_BSHUF=OFF \
             -DENABLE_BZIP2=OFF \

.github/workflows/main-package-managers-win.yml

@@ -136,6 +136,7 @@ jobs:
             -DENABLE_ZSTD=ON \
             -DENABLE_BITGROOM=OFF \
             -DENABLE_GRANULAR_BITROUND=OFF \
+            -DENABLE_BITROUND=OFF \
             -DENABLE_BSHUF=OFF \
             $GITHUB_WORKSPACE
           cmake --build . --parallel 4 --config ${{ inputs.build_mode }}

BITROUND/Additional_Legal/LICENSE

@@ -0,0 +1,51 @@
+HDF5 BitRound filter plugin -- provenance and license
+======================================================
+
+This plugin adapts two BSD-style sources, both authored by Charlie Zender:
+
+  * the BitRound quantization core, from netcdf-c (libsrc4/nc4var.c,
+    NC_QUANTIZE_BITROUND; PR #2232). The netcdf-c repository is copyright
+    UCAR (University Corporation for Atmospheric Research).
+
+  * the HDF5 filter-plugin scaffolding (cd_values layout, set_local /
+    can_apply pattern), from the BitGroom plugin in the ccr project,
+    copyright (c) Charlie Zender / ccr.
+
+Algorithm reference:
+  Kloewer M, Razinger M, Dominguez JJ, Dueben PD, Palmer TN. "Compressing
+  atmospheric data into its real information content." Nat. Comput. Sci.
+  1(11), 713-724 (2021). doi:10.1038/s43588-021-00156-2
+
+Both upstream sources are distributed under the BSD 3-Clause License, which
+also governs this plugin:
+
+BSD 3-Clause License
+
+Copyright (c) 2019, ccr
+Copyright (c) UCAR (netcdf-c)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

BITROUND/CMakeLists.txt

@@ -0,0 +1,165 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+cmake_minimum_required (VERSION 3.18)
+project (H5BITROUND C)
+
+if (POLICY CMP0074)
+  # find_package() uses <PackageName>_ROOT variables.
+  cmake_policy (SET CMP0074 NEW)
+endif ()
+
+if (POLICY CMP0083)
+  # To control generation of Position Independent Executable (PIE) or not,
+  # some flags are required at link time.
+  cmake_policy (SET CMP0083 NEW)
+endif ()
+
+# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
+if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
+    cmake_policy(SET CMP0135 NEW)
+endif()
+
+#-----------------------------------------------------------------------------
+# Basic H5BITROUND stuff here
+#-----------------------------------------------------------------------------
+if (NOT H5PL_RESOURCES_DIR)
+  include (${H5BITROUND_SOURCE_DIR}/config/cmake/HDFMacros.cmake)
+  include (${H5BITROUND_SOURCE_DIR}/config/cmake/HDFPluginMacros.cmake)
+  include (${H5BITROUND_SOURCE_DIR}/config/CacheURLs.cmake)
+
+  SET_HDF_BUILD_TYPE()
+endif ()
+BASIC_SETTINGS (H5${BITROUND_PACKAGE_NAME})
+
+set (H5BITROUND_VERS_MAJOR 1)
+set (H5BITROUND_VERS_MINOR 0)
+set (H5BITROUND_VERS_RELEASE 0)
+
+set (H5BITROUND_SOVERS_MAJOR 1)
+set (H5BITROUND_SOVERS_MINOR 0)
+set (H5BITROUND_SOVERS_INTERFACE 1)
+set (H5BITROUND_SOVERS_RELEASE 0)
+math (EXPR H5BITROUND_SOVERS_MAJOR ${H5BITROUND_SOVERS_INTERFACE}-${H5BITROUND_SOVERS_RELEASE})
+
+#-----------------------------------------------------------------------------
+set (H5BITROUND_PACKAGE_VERSION "${H5BITROUND_VERS_MAJOR}.${H5BITROUND_VERS_MINOR}")
+set (H5BITROUND_PACKAGE_VERSION_STRING "${H5BITROUND_PACKAGE_VERSION}")
+set (H5BITROUND_PACKAGE_VERSION_MAJOR "${H5BITROUND_VERS_MAJOR}")
+set (H5BITROUND_PACKAGE_VERSION_MINOR "${H5BITROUND_VERS_MINOR}")
+set (H5BITROUND_PACKAGE_STRING "${H5BITROUND_PACKAGE_NAME} ${H5BITROUND_PACKAGE_VERSION}")
+set (H5BITROUND_PACKAGE_TARNAME "${H5BITROUND_PACKAGE_NAME}{HDF_PACKAGE_EXT}")
+set (H5BITROUND_PACKAGE_URL "http://www.hdfgroup.org")
+set (H5BITROUND_PACKAGE_BUGREPORT "help@hdfgroup.org")
+set (H5BITROUND_PACKAGE_SOVERSION "${H5BITROUND_SOVERS_MAJOR}.${H5BITROUND_SOVERS_RELEASE}.${H5BITROUND_SOVERS_MINOR}")
+set (H5BITROUND_PACKAGE_SOVERSION_MAJOR "${H5BITROUND_SOVERS_MAJOR}")
+message(STATUS "Configuring for bitround HDF5 Plugin version: " ${H5BITROUND_PACKAGE_STRING})
+
+#-----------------------------------------------------------------------------
+# Include some macros for reusable code
+#-----------------------------------------------------------------------------
+include (${H5BITROUND_RESOURCES_DIR}/H5BITROUNDMacros.cmake)
+
+#-----------------------------------------------------------------------------
+# Run all the CMake configuration tests for our build environment
+#-----------------------------------------------------------------------------
+include (${H5BITROUND_RESOURCES_DIR}/ConfigureChecks.cmake)
+
+#-----------------------------------------------------------------------------
+# HDF5 support
+#-----------------------------------------------------------------------------
+HDF5_SUPPORT (TRUE)
+message (STATUS "H5BITROUND link libs: ${H5PL_LINK_LIBS}")
+
+#-----------------------------------------------------------------------------
+# Generate the bitround_config.h file containing user settings needed by compilation
+#-----------------------------------------------------------------------------
+configure_file (${H5BITROUND_RESOURCES_DIR}/config.h.in ${H5BITROUND_BINARY_DIR}/bitround_config.h @ONLY)
+
+include (ExternalProject)
+set (H5PL_ALLOW_EXTERNAL_SUPPORT "NO" CACHE STRING "Allow External Library Building (NO GIT TGZ)")
+set_property (CACHE H5PL_ALLOW_EXTERNAL_SUPPORT PROPERTY STRINGS NO GIT TGZ)
+#-----------------------------------------------------------------------------
+option (BUILD_BITROUND_LIBRARY_SOURCE "build the bitround library within the plugin" ON)
+if (NOT BUILD_BITROUND_LIBRARY_SOURCE)
+  if (H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+    option (BITROUND_USE_EXTERNAL "Use External Library Building for BITROUND" 1)
+    if (H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT") 
+      message (FATAL_ERROR " BITROUND has no compression only library repository")
+    elseif (H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+      if (NOT H5PL_COMP_TGZPATH)
+        set (H5PL_COMP_TGZPATH ${H5BITROUND_SOURCE_DIR})
+      endif ()
+      set (BITROUND_URL ${H5PL_COMP_TGZPATH}/${BITROUND_TGZ_NAME})
+    else ()
+      set (BITROUND_USE_EXTERNAL 0)
+    endif ()
+  endif ()
+  #-----------------------------------------------------------------------------
+  # bitround Library Settings
+  #-----------------------------------------------------------------------------
+  if (NOT H5_BITROUND_HEADER)
+    if (NOT BITROUND_USE_EXTERNAL)
+      find_package (BITROUND NAMES ${BITROUND_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static)
+      if (NOT BITROUND_FOUND)
+        find_package (BITROUND) # Legacy find
+        if (BITROUND_FOUND)
+          set (H5PL_LINK_LIBS ${H5PL_LINK_LIBS} ${BITROUND_LIBRARIES})
+        endif ()
+      endif ()
+    endif ()
+    if (BITROUND_FOUND)
+      set (H5_HAVE_BITROUND 1)
+      set (BITROUND_INCLUDE_DIR_GEN ${BITROUND_INCLUDE_DIR})
+      set (BITROUND_INCLUDE_DIRS ${BITROUND_INCLUDE_DIRS} ${BITROUND_INCLUDE_DIR})
+    else ()
+      if (H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR H5PL_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+        EXTERNAL_BITROUND_LIBRARY (${H5PL_ALLOW_EXTERNAL_SUPPORT})
+        set (H5_HAVE_BITROUND 1)
+        message (STATUS "Filter BITROUND is built")
+      else ()
+        message (FATAL_ERROR " BITROUND is Required for ${H5BITROUND_PACKAGE_NAME} library")
+      endif ()
+    endif ()
+  endif ()
+  message (STATUS "bitround found: INC=${BITROUND_INCLUDE_DIR} TOOLS=${BITROUND_LIBRARIES}")
+  set (H5PL_LINK_LIBS ${H5PL_LINK_LIBS} ${BITROUND_LIBRARIES})
+
+  if (BITROUND_FOUND)
+    PACKAGE_BITROUND_LIBRARY (${H5PL_ALLOW_EXTERNAL_SUPPORT})
+  endif ()
+endif ()
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
+# Dashboard and Testing Settings
+#-----------------------------------------------------------------------------
+option (H5PL_BUILD_TESTING "Build h5bitround Unit Testing" OFF)
+if (H5PL_BUILD_TESTING)
+  set (DART_TESTING_TIMEOUT 1200 CACHE STRING
+       "Timeout in seconds for each test (default 1200=20minutes)")
+  enable_testing ()
+  include (CTest)
+  include (${PROJECT_SOURCE_DIR}/CTestConfig.cmake)
+  configure_file (${${PLUGIN_PACKAGE_NAME}_RESOURCES_DIR}/CTestCustom.cmake ${PROJECT_BINARY_DIR}/CTestCustom.ctest @ONLY)
+endif ()
+
+add_subdirectory (src)
+
+option (H5PL_BUILD_EXAMPLES "Build h5bitround Examples" OFF)
+if (H5PL_BUILD_EXAMPLES)
+  add_subdirectory (example)
+endif ()
+
+#-----------------------------------------------------------------------------
+# Add file(s) to CMake Install
+#-----------------------------------------------------------------------------
+INSTALL_SUPPORT (H5BITROUND)

BITROUND/CTestConfig.cmake

@@ -0,0 +1,36 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   ENABLE_TESTING()
+##   INCLUDE(CTest)
+set (CTEST_PROJECT_NAME "HDF5PLUGINS")
+set (CTEST_NIGHTLY_START_TIME "18:00:00 CST")
+
+set (CTEST_DROP_METHOD "https")
+set (CTEST_DROP_SITE "cdash.hdfgroup.org")
+set (CTEST_DROP_LOCATION "/submit.php?project=HDF5PLUGINS")
+set (CTEST_DROP_SITE_CDASH TRUE)
+
+set (UPDATE_TYPE git)
+set (VALGRIND_COMMAND "/usr/bin/valgrind")
+set (VALGRIND_COMMAND_OPTIONS "-v --tool=memcheck --leak-check=full --track-fds=yes --num-callers=50 --show-reachable=yes --track-origins=yes --malloc-fill=0xff --free-fill=0xfe")
+
+set (CTEST_TEST_TIMEOUT 3600 CACHE STRING
+    "Maximum time allowed before CTest will kill the test.")
+set (DART_TESTING_TIMEOUT 3600 CACHE STRING
+    "Maximum time allowed before CTest will kill the test." FORCE)
+
+set (CTEST_SUBMIT_RETRY_DELAY 20 CACHE STRING
+    "How long to wait between timed-out CTest submissions.")

BITROUND/Makefile.am

@@ -0,0 +1,13 @@
+# Copyright by The HDF Group. All rights reserved.
+
+# This builds the main BITROUND directory. This is the bitround
+# filter. It's similar to the built in HDF5 shuffle filter, but works
+# on a bit level instead of bytes.
+
+# Allen Byrne, Ed Hartnett 1/15/19
+
+# This directory stores libtool macros, put there by aclocal.
+ACLOCAL_AMFLAGS = -I m4
+
+# Build these subdirectories.
+SUBDIRS = src #example